rs7780294

Variant names:

• chr7-128736608-C-T
• rs7780294

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.107 in 152,190 control chromosomes in the GnomAD database, including 1,918 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.11 (1918 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16283 AN: 152072 Hom.: 1916 Cov.: 33

Gnomad AFR AF: 0.0424

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0762

Gnomad OTH AF: 0.0986

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.107 AC: 16296 AN: 152190 Hom.: 1918 Cov.: 33 AF XY: 0.114 AC XY: 8513 AN XY: 74416

Gnomad4 AFR AF: 0.0423

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.0519

Gnomad4 EAS AF: 0.586

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.0762

Gnomad4 OTH AF: 0.0999

Alfa AF: 0.0906 Hom.: 1397

Bravo AF: 0.119

Asia WGS AF: 0.356 AC: 1236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.24
DANN	Benign	0.64

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7780294; hg19: chr7-128376662;